Research workbench
Crystal structure of benzamide 9 bound to auroraa
Analyse Crystal structure of benzamide 9 bound to auroraa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O50
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdna FLJ58295, highly similar to SERINE/THREONINE-protein kinase 6
- EC
- 2.7.11.1
- UniProt
- B4DX16
- Ligands
- LJE
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cdna FLJ58295, highly similar to SERINE/THREONINE-protein kinase 6 (EC 2.7.11.1) | protein | 246 | 43% helix, 19% strand | B4DX16 |
| B | Cdna FLJ58295, highly similar to SERINE/THREONINE-protein kinase 6 (EC 2.7.11.1) | protein | 249 | 42% helix, 18% strand | B4DX16 |
Ligands and binding sites
- LJE · N-{3-methyl-4-[(3-pyrimidin-4-ylpyridin-2-yl)oxy]phenyl}-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.72 | 0.79 | 58 | LJE |
| 2 | 394 | 0.65 | 0.78 | 38 | LJE |
| 3 | 141 | 0.58 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 411 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3O50 · Crystal structure of benzamide 9 bound to AuroraA · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B4DX16
- Elsewhere: RCSB PDB 3O50 · PDBe 3O50 · UniProt B4DX16
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